Geology – Geodes in cross-section. Geodes are geological secondary sedimentary structures which occur in sedimentary and volcanic rocks. Geodes are spherical masses of minerals that were deposited syngenetically within rock formations. Inside the chalcedony shell are minerals such as calcite, pyrite, kaolinite, sphalerite, millerite, barite, dolomite, amethyst, smithsonite and quartz.